How to evaluate the interaction between epoxy and a free surface via metadynamics: a coarse-grained example - dataset

Abstract:
from [1]

Molecular investigations into polymer-surface interactions are essential for understanding and optimizing the mechanical
behavior of, e.g., adhesive joints or polymer nanocomposites. In this context, metadynamics provides a powerful tool for
determining the free energy of a molecular system through Gaussian sampling. While the literature demonstrates that
metadynamics is well suited for adherend–adhesive systems, there is little discussion on the choice of the metadynamics
parameters and their impact on the resulting free energy. This contribution provides a step-by-step methodology for
determining the parameters of metadynamics, specifically the Gaussian’s depth, width, and deposition time, as well as the
convergence. To illustrate this process, we utilize a simple coarse-grained system made up of a rigid substrate and either
an epoxy or hardener molecule. Once we establish the optimal metadynamics parameters, we examine the effects of
non-bonded polymer-surface interactions, which are modeled using 12-6 Lennard–Jones potentials, on the resulting free
energy surface. As expected, we find that the distance parameter σps influences both the position and depth of the free
energy well, while the energy parameter εps only affects the well depth. The methodology outlined here can be applied
to more complex systems, making this article a useful guide for advanced studies on adhesive joints and polymer surface
interactions in general.

Contact:

Maximilian Ries
Institute of Applied Mechanics
Friedrich-Alexander-Universität Erlangen-Nürnberg
Egerlandstr. 5
91058 Erlangen

Software:

All MD simulations were performed with LAMMPS [2,3], version: 12 June 2025
All Metadynamics simulations used the PLUMED [4,5] library (v2.9.4)

License:

Creative Commons Attribution 4.0 International

Context:

Data set supplementing  journal paper:
[1] M. Ries,  "How to evaluate the interaction between epoxy and a free surface via metadynamics: A coarse-grained example" Mathematics and Mechanics of Solids (2026)DOI: 10.1177/10812865261429388

Content:

Structure of the data set:

    01_metadynamics
        01_width            results corresponding to Section 3.1
            DGEBA            simulation folder
            PACM            simulation folder
        02_height            results corresponding to Section 3.3
            DGEBA            simulation folder
            PACM            simulation folder
        03_eps-sigma        results corresponding to Section 3.2 & 3.4
            DGEBA            simulation folder
            PACM            simulation folder
        
    02_umbrella_sampling    results corresponding to Section 3.2
    
Each simulation folder contains
    execute_lmp.sh            bash file to start lammps/metad runs
    main.in                    lammps input file
    potential_coeff.in        file containing force field parameters
    Standard_Input            folder containing pre-equilibrated PACM & DGEBA molecules
    OUT*                    output folders, named after main parameters; containing main result files, i.e., tracking collective variables, and all information to assemble the free energy surface
    

References:

[1] M. Ries,  "How to evaluate the interaction between epoxy and a free surface via metadynamics: A coarse-grained example" Mathematics and Mechanics of Solids (2026)DOI: 10.1177/10812865261429388

[2] S. Plimpton, “Fast parallel algorithms for short-range molecular dynamics,” Journal of computational physics, 1995, 117, 1-19.

[3] A. P. Thompson et al., “LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales,” Computer Physics Communications, vol. 271, p. 108171, 2022.

[4] consortium, TP. Promoting transparency and reproducibility in enhanced molecular simulations. Nat Methods 2019; 16(8): 670–673.

[5] Tribello, GA, Bonomi, M, Branduardi, D, et al. PLUMED 2: new feathers for an old bird. Comput Phys Commun 2014; 185(2): 604–613.